X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XR8PDB ENTRY 2XR8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16PEG 8K, PIPES BUFFER PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.350

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.472α = 102.51
b = 133.585β = 104.99
c = 133.229γ = 102.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2125900.068.92.43778672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2564.30.3521.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2XR82.212535886118986900.2170.2150.266RANDOM30.43
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.230.12-1.34-1.33-0.950.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.246
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg15.599
r_dihedral_angle_1_deg6.298
r_scangle_it1.8
r_angle_refined_deg1.196
r_scbond_it1.175
r_mcangle_it0.744
r_mcbond_it0.463
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.246
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg15.599
r_dihedral_angle_1_deg6.298
r_scangle_it1.8
r_angle_refined_deg1.196
r_scbond_it1.175
r_mcangle_it0.744
r_mcbond_it0.463
r_nbtor_refined0.301
r_xyhbond_nbd_refined0.221
r_nbd_refined0.195
r_symmetry_hbond_refined0.179
r_symmetry_vdw_refined0.169
r_metal_ion_refined0.133
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms59327
Nucleic Acid Atoms
Solvent Atoms2524
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing